Modelling process uncertainty

Example: Ebola forecasting in 2014-16

The unknown

• Community/hospital/funeral transmission
• Spatial dynamics
• Changes in behaviour
• Changes in reporting
• Interventions
• Seasonality
• etc

The known

• Average incubation period (~9 days)
• Average infectious period (~11 days)
• Case-fatality rate (~70%)

WHO Ebola response team (2014)

Transmission intensity as a stochastic process

\(d\log(R_0(t)) = \sigma dW_t\)

Dureau (2013)

Particle MCMC

• Method for filtering trajectories consistent with data
• Highly parallelisable

Andrieu (2010), Murray (2013)

Particle filter to estimate posterior trajectories

Filtered trajectories tell us something about dynamics